Dihydrolipoamide dehydrogenase



General
Dihyrolipoamide dehydrogenase (E3) is a part of the multienzyme complex of pyruvate dehydrogenase. This multienzyme complex catalyzes the formation of Acetyl-CoA from pyruvate via oxidative decarboxylation.

Structure
In E. coli this complex exists as 24 E2 proteins arranged in a cube, surrounded by 12 E1 proteins and 12 E3 proteins. Dihidrolipoamide dehydrogenase (E3) binds to the pyruvate dehydrogenase complex (and the center of the cube of E2 proteins) through a coupling with E3 binding protein .‘ ’ The E3 binding protein is a completely separate protein from E3, but serves to connect the E3 polypeptides to the overarching structure. The active site includes an FAD group, as well as Cys 43 and Cys 48 forming a disulfide bond. When the substrate is not present, Tyr 181 “covers” the catalytic site from being exposed to solvents. Dihidrolipoamide dehydrogenase (E3) is a SCOP alpha and beta (a/b) class protein of the FAD/NAD(P)-binding domain fold.

Mechanism
The redox reaction occurs through the influence of Cys 43 and Cys 48, between which there is a disulfide bond within a distorted alpha helix. This redox active disulfide bond becomes reduced in order to reoxidize the E2 enzyme of the multienzyme complex.‘ ’ E2 donates protons and electrons to E3 in order to complete its catalytic cycle. The E3 enzyme’s flavin ring (FAD) funnels electrons from the disulfide bond to itself, then binds to NAD+ and donates electrons, reoxidizing the E3, and leaving it ready for the beginning of its catalytic cycle again.

Regulation
The regulation of Dihidrolipoamide dehydrogenase (E3) kinetically comes through regulation of the entire Pyruvate Dehydrogenase complex. As would be expected, one of the main regulators is the presence of its product, acetyl-CoA as well as NADH. This is through the E1 reaction of the complex, but necessarily effects the E3 reaction. However, the E1 portion of the complex is also regulated by phosphatase and kinase in phosphorylation and dephosphorylation reactions.‘ ’

3D structures of dihydrolipoamide dehydrogenase
3ic9 – DLD – Colwellia psychrerythraea

2qae – DLD – Trypanosoma cruzi

2ihw – bDLD E2 - bovine

2eq6 – TtDLD – Thermus thermophilus

2yqu – TtDLD E3

2eq7, 2eq8, 2eq9 – TtDLD E2+E3

1ivi – DLD – pig

1jeh – yDLD E3 – yeast

1dxl – DLD – pea

1lpf – DLD – Pseudomonas fluorescens

3lad – DLD – Azotobacter vinelandii

3l60 – MtDLD E2 – Mycobacterium tuberculosis

2a8x - MtDLD E3

DLD binary complexes
2ii3, 2ii4, 2ii5 – bDLD + CoA

3rnm – hDLD subunit-binding domain + dihydrolipoyl dehydrogenase – human

2f5z, 1zy8 – hDLD E3 + pyruvate dehydrogenase E3-binding domain

1zmc, 1zmd – hDLD + NAD

1v59 – yDLD + NAD

1lvl – DLD + NAD – Pseudomonas putida

3ii4 – MtDLD + inhibitor

1ebd – DLD + dihydrolipoamide acetyltransferase binding domain – Geobacillus stearothermophilus